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Protein

Nigerythrin

Gene

ngr

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Exhibits NADH peroxidase activity (in vitro).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi40 – 401Iron 1
Metal bindingi73 – 731Iron 1
Metal bindingi73 – 731Iron 2
Metal bindingi115 – 1151Iron 2
Metal bindingi118 – 1181Iron 1
Metal bindingi149 – 1491Iron 1
Metal bindingi149 – 1491Iron 2
Metal bindingi152 – 1521Iron 2
Metal bindingi174 – 1741Iron 3
Metal bindingi177 – 1771Iron 3
Metal bindingi189 – 1891Iron 3
Metal bindingi192 – 1921Iron 3

GO - Molecular functioni

Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciDVUL882:GJIL-20-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Nigerythrin
Gene namesi
Name:ngr
Ordered Locus Names:DVU_0019
OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000002194 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 202202NigerythrinPRO_0000135072Add
BLAST

Proteomic databases

PaxDbiP30820.

Interactioni

Subunit structurei

Homodimer. May possess two rubredoxin-like centers and two hemerythrin-like binuclear-iron centers per dimer.

Protein-protein interaction databases

STRINGi882.DVU0019.

Structurei

Secondary structure

1
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni10 – 123Combined sources
Helixi29 – 5628Combined sources
Helixi60 – 8728Combined sources
Helixi104 – 12017Combined sources
Helixi122 – 13312Combined sources
Helixi136 – 16126Combined sources
Turni162 – 1643Combined sources
Beta strandi171 – 1733Combined sources
Beta strandi175 – 1773Combined sources
Beta strandi180 – 1845Combined sources
Turni190 – 1923Combined sources
Helixi196 – 1983Combined sources
Beta strandi200 – 2023Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YUXX-ray1.60A/B1-202[»]
1YUZX-ray1.40A/B1-202[»]
1YV1X-ray1.50A/B1-202[»]
ProteinModelPortaliP30820.
SMRiP30820. Positions 1-202.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP30820.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini23 – 168146Ferritin-like diironPROSITE-ProRule annotationAdd
BLAST
Domaini169 – 20234Rubredoxin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ferritin-like diiron domain.PROSITE-ProRule annotation
Contains 1 rubredoxin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4108RAC. Bacteria.
COG1592. LUCA.
OMAiKVFLCPV.
OrthoDBiEOG69SKK0.
PhylomeDBiP30820.

Family and domain databases

Gene3Di1.20.1260.10. 1 hit.
2.20.28.10. 1 hit.
InterProiIPR009040. Ferritin-like_diiron.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR003251. Rubrerythrin.
[Graphical view]
PfamiPF02915. Rubrerythrin. 1 hit.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS50905. FERRITIN_LIKE. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P30820-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVRAQVPTV KNATNFNMVA DSKTAVGSTL ENLKAAIAGE TGAHAKYTAF
60 70 80 90 100
AKAAREQGYE QIARLFEATA AAELIHIGLE YALVAEMEPG YEKPTVAAPS
110 120 130 140 150
AYSCDLNLIS GANGEIYETS DMYPAFIRKA QEEGNSKAVH VFTRAKLAES
160 170 180 190 200
VHAERYLAAY NDIDAPDDDK FHLCPICGYI HKGEDFEKCP ICFRPKDTFT

AY
Length:202
Mass (Da):22,098
Last modified:May 24, 2004 - v3
Checksum:iDF5410519EE8D899
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti129 – 1291K → E in AAC45480 (PubMed:9226272).Curated
Sequence conflicti132 – 1321E → G in AAC45480 (PubMed:9226272).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U71215 Genomic DNA. Translation: AAC45480.1.
AE017285 Genomic DNA. Translation: AAS94503.1.
RefSeqiWP_010937330.1. NC_002937.3.
YP_009244.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS94503; AAS94503; DVU_0019.
GeneIDi2794280.
KEGGidvu:DVU0019.
PATRICi32060008. VBIDesVul119526_0016.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U71215 Genomic DNA. Translation: AAC45480.1.
AE017285 Genomic DNA. Translation: AAS94503.1.
RefSeqiWP_010937330.1. NC_002937.3.
YP_009244.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YUXX-ray1.60A/B1-202[»]
1YUZX-ray1.40A/B1-202[»]
1YV1X-ray1.50A/B1-202[»]
ProteinModelPortaliP30820.
SMRiP30820. Positions 1-202.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi882.DVU0019.

Proteomic databases

PaxDbiP30820.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS94503; AAS94503; DVU_0019.
GeneIDi2794280.
KEGGidvu:DVU0019.
PATRICi32060008. VBIDesVul119526_0016.

Phylogenomic databases

eggNOGiENOG4108RAC. Bacteria.
COG1592. LUCA.
OMAiKVFLCPV.
OrthoDBiEOG69SKK0.
PhylomeDBiP30820.

Enzyme and pathway databases

BioCyciDVUL882:GJIL-20-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP30820.

Family and domain databases

Gene3Di1.20.1260.10. 1 hit.
2.20.28.10. 1 hit.
InterProiIPR009040. Ferritin-like_diiron.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR003251. Rubrerythrin.
[Graphical view]
PfamiPF02915. Rubrerythrin. 1 hit.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS50905. FERRITIN_LIKE. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris (Hildenborough)."
    Lumppio H.L., Shenvi N.V., Garg R.P., Summers A.O., Kurtz D.M. Jr.
    J. Bacteriol. 179:4607-4615(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
  3. "Nigerythrin and rubrerythrin from Desulfovibrio vulgaris each contain two mononuclear iron centers and two dinuclear iron clusters."
    Pierik A.J., Wolbert R.B.G., Portier G.L., Verhagen M.F.J.M., Hagen W.R.
    Eur. J. Biochem. 212:237-245(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-15.
  4. "High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins."
    Iyer R.B., Silaghi-Dumitrescu R., Kurtz D.M. Jr., Lanzilotta W.N.
    J. Biol. Inorg. Chem. 10:407-416(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS), IRON-BINDING SITES.

Entry informationi

Entry nameiNIGY_DESVH
AccessioniPrimary (citable) accession number: P30820
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: May 24, 2004
Last modified: November 11, 2015
This is version 109 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.